Contacts of the helix formed by residues 213 - 226 (chain C) in PDB entry 1MKD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C SER* 2.9 26.9 + - - +
211C GLY 4.0 5.5 + - - +
212C ASN* 1.3 84.9 + - - +
214C PRO* 1.3 67.3 - - - +
215C LEU 3.3 2.5 - - - -
216C THR* 3.4 3.9 + - + -
217C VAL* 3.0 28.9 + - + +
244C MET* 3.0 63.8 + - + +
247C GLU* 3.4 26.4 - - - +
248C ASP* 2.8 27.5 + - - -
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Residues in contact with PRO 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 4.5 6.1 - - + +
206C ILE* 4.5 5.2 - - + -
207C ALA* 3.9 28.0 - - + +
210C SER* 3.4 6.2 - - - +
212C ASN* 3.3 4.9 - - - -
213C ARG* 1.3 90.9 - - - +
215C LEU* 1.3 57.7 + - - +
217C VAL* 4.5 3.8 - - + -
218C ILE* 2.8 42.9 + - + +
247C GLU* 3.1 7.4 - - - +
259C ASN* 3.2 28.7 - - - +
260C ILE* 4.1 11.4 - - + -
263C ALA* 3.7 11.7 - - + -
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C PRO* 1.3 79.3 - - - +
216C THR* 1.3 58.5 + - - +
218C ILE* 6.2 0.2 - - + -
219C MET* 2.8 54.6 + - + +
243C LEU* 5.0 3.6 - - + +
246C LEU* 4.0 19.5 - - + -
247C GLU* 2.9 27.9 + - + +
250C TYR* 3.8 33.2 - - + -
259C ASN* 3.9 7.6 - - + +
262C ALA* 3.9 6.1 - - + -
263C ALA* 3.6 27.5 - - - +
266C VAL* 3.9 13.0 - - + -
295C ALA* 4.0 5.4 - - + +
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Residues in contact with THR 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ARG* 3.9 10.0 - - - -
215C LEU* 1.3 72.4 - - - +
217C VAL* 1.3 65.5 + - + +
220C HIS* 3.0 28.1 + - + +
240C ILE* 4.6 11.9 - - + -
243C LEU* 3.4 45.7 + - + +
244C MET* 3.6 34.5 + - + +
247C GLU* 2.6 29.3 + - - -
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Residues in contact with VAL 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LEU* 4.6 11.4 - - + -
193C LEU* 3.4 37.7 - - + -
206C ILE* 4.5 7.0 - - + -
210C SER* 3.7 21.1 - - - -
213C ARG* 3.0 24.0 + - + +
214C PRO* 3.9 4.3 - - + +
216C THR* 1.3 80.2 - - + +
218C ILE* 1.3 52.0 + - - +
220C HIS* 3.7 4.5 - - - +
221C THR* 2.7 36.1 + - + +
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Residues in contact with ILE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LEU* 4.2 16.8 - - + -
196C VAL* 4.7 4.5 - - + -
201C LEU* 4.1 17.0 - - + -
203C VAL* 4.0 18.4 - - + -
206C ILE* 4.3 11.4 - - + -
214C PRO 2.8 26.5 + - - +
215C LEU 4.2 0.7 - - - +
217C VAL* 1.3 69.8 - - - +
219C MET* 1.3 67.3 + - - +
221C THR* 3.0 6.5 + - - -
222C ILE* 2.9 43.9 + - + +
263C ALA* 3.9 27.4 - - + +
266C VAL* 4.7 2.7 - - + -
267C GLN* 4.2 16.8 - - + +
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Residues in contact with MET 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LEU* 2.8 41.7 + - + +
218C ILE* 1.3 70.9 - - - +
220C HIS* 1.3 58.4 + - - +
222C ILE* 3.1 4.8 + - - -
223C PHE* 2.9 63.0 + - + -
239C LEU* 5.5 0.7 - - + -
242C TYR* 6.2 0.9 - - + -
243C LEU* 3.5 34.1 - - + -
246C LEU* 5.7 0.4 - - + -
266C VAL* 3.6 24.0 - - + -
291C ILE* 3.9 15.7 - - + +
292C PHE* 4.6 11.2 - - + -
295C ALA* 3.6 24.2 - - + -
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Residues in contact with HIS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C THR* 3.0 21.2 + - + +
217C VAL* 3.7 5.1 + - - +
219C MET* 1.3 76.6 - - - +
221C THR* 1.3 63.6 + - + +
223C PHE* 3.2 7.2 + - - +
224C GLN* 3.0 67.3 + - + +
229C LEU* 4.7 0.7 - - + -
236C VAL* 4.0 14.2 - - + +
239C LEU* 4.2 12.8 - - + -
240C ILE* 3.5 29.3 - - + +
243C LEU* 3.9 9.1 - - + +
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Residues in contact with THR 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LEU* 3.7 38.9 - - + +
196C VAL* 4.8 11.8 - - - +
217C VAL* 2.7 18.5 + - + +
218C ILE* 3.0 16.3 + - - +
220C HIS* 1.3 82.2 - - - +
222C ILE* 1.3 55.5 + - - +
224C GLN* 3.5 9.3 + - + +
225C GLU* 2.9 29.0 + - - +
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Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C VAL* 3.6 19.3 - - + -
218C ILE* 2.9 38.0 + - + +
219C MET* 3.7 4.7 - - - +
221C THR* 1.3 74.1 - - - +
223C PHE* 1.3 63.2 + - + +
225C GLU* 3.4 6.0 - - - +
226C ARG* 2.8 30.0 + - - +
266C VAL* 3.8 19.3 - - + -
267C GLN* 4.0 6.1 - - - -
270C HIS* 3.4 46.0 - - + +
291C ILE* 4.0 25.4 - - + -
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Residues in contact with PHE 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C MET* 2.9 56.0 + - + +
220C HIS 3.6 4.7 - - - +
222C ILE* 1.3 74.0 - - + +
224C GLN* 1.3 61.9 + - - +
226C ARG 3.4 0.2 + - - -
227C ASP* 2.9 23.6 + - - -
228C LEU* 3.0 34.9 + - + -
229C LEU* 4.0 11.0 + - + -
234C ILE* 3.8 25.4 - - + -
239C LEU* 3.8 35.7 - - + -
288C LEU* 3.8 25.8 - - + -
291C ILE* 4.1 17.7 - - + -
292C PHE* 5.7 2.9 - - + -
345C ILE* 5.2 10.8 - - + -
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Residues in contact with GLN 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C HIS* 3.0 53.7 + - + +
221C THR* 3.6 10.8 - - + +
223C PHE* 1.3 75.8 - - - +
225C GLU* 1.3 65.2 + - - +
227C ASP* 2.9 17.3 + - - +
229C LEU* 3.2 23.4 - - - +
236C VAL* 4.9 6.1 - - - +
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C VAL* 4.5 9.7 - - + +
197C ASN* 3.4 37.7 + - - +
221C THR 2.9 19.2 + - - +
222C ILE* 3.4 8.3 - - - +
224C GLN* 1.3 77.4 - - - +
226C ARG* 1.3 59.7 + - + +
227C ASP* 3.6 1.0 + - - +
270C HIS* 4.1 13.7 - - + +
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Residues in contact with ARG 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ILE* 2.8 20.4 + - - +
225C GLU* 1.3 73.9 - - + +
227C ASP* 1.3 70.9 + - - +
228C LEU* 3.0 23.2 + - + +
231C THR* 4.7 2.1 + - - -
270C HIS* 2.9 42.2 + - + -
273C LEU* 3.5 16.3 + - - +
274C SER* 2.9 28.2 + - - +
284C ASP* 5.6 1.7 - - - +
287C ILE* 3.9 34.1 - - - +
291C ILE* 3.6 25.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il